Ham string flexibility is always a good place to start - stretch.
There are a few other things to check when you have pain there:
1: shoes. Make sure your shoes give good arch support and consider the use of varus wedges. To demonstrate, look at your lower leg and rotate your foot so your arch lifts, you will see that your lower leg rotates, and when it does the bony part you say hurts becomes less prominent. This means as tendons can glide over it more easily. not all bike fitters will be able to advise on this and it is often a matter of trial and error. check out specialised web site for details of shoes and more info
2: Stance width. the lateral collateral ligament connects in that area and may be over worked if you stance width is too narrow. I have had difficulty with this. Try putting a few washers between pedal and crank and setting your cleats to the inside of the shoe to get more stance width.
3: The IT band also connects in close proximity to the Lateral collateral ligament and it can be difficult to know exactly where pain is comming from. google up some stretches to help that too or try using a foam roller.
The fact you have had a bike fit means your basics should be close to right but many fitters wont advise on the above because it is extremely difficult to determine by looking at someone. I have posted here based on my own direct experience so take it or leave it, I have no medical knowledge, just 20 years of enjoying cycling and various knee issues.
If you still have pain then go very easy on the training until you have sorted the problem. It band issues in particular are very difficult to get rid of once they start. also be aware you might have it set up correctly and just need a few more base miles before things settle down.
good luck
